An option we found particularly enjoyable - we had several hours to kill in Athens - was to take the Metro from the airport to Monastiraki, stow our luggage in the left-luggage lockers there (it's one of only 2 or 3 Metro stations that has these lockers) and walk up to the Acropolis: an easy climb through some very attractive corners of old Athens. Then the Metro again from Monastiraki to Piraeus. You have to change trains anyway at Monastiraki.
A word of warning however: the cheapest way to do this appears to be to get a ticket from the Airport to Piraeus and just break your journey at Monastiraki (a ticket for 2 people costs €10). DON'T! The Metro tickets have to be validated by sticking them in a time-stamping machine before you board the train: they are then valid for travel for all of 90 minutes. Even if you're simply changing trains at Monastiraki, rather than actually breaking the journey there, you may well only just about complete the trip in 90 minutes. And if you're caught with an "expired" ticket the fine is €40 per person. You can appeal by email (tricky, because the Inspectors will give you the wrong email address) when you get home, and if you do so nicely, the fines office *may* let you off. But the whole procedure takes a lot of time and leaves a rather unpleasant flavour. As you may have guessed, I speak from experience! Get one ticket to Monastiraki; then when you get back there after your wanderings, get a new ticket to complete the journey.
Flying to Athens. For those who haven't tried it, it's much easier and cheaper than flying to Crete!! You don't have to travel with dear old Olympic if you don't like them: BA go from Heathrow, Gatwick and Manchester; EasyJet from Gatwick, Luton and Manchester; Aegean (haven't seen many mentions of them on this forum but perhaps I'm going blind) - "Airline of the Year 2008" - from Stanstead, and they're better all round as well as cheaper than Olympic.
If the fast ferry is the only option to Rethymno when you're going and it doesn't appeal, some *very* plush Anek ferries go overnight to Haniá and, I believe, to Iraklion. IMHO it's MUCH the best way of getting to Crete....
Sorry this has been so long - hope it gives someone some help/ideas.